10.6084/M9.FIGSHARE.C.6259510
Daphne Z. Hoh
Daphne Z.
Hoh
Academia Sinica
National Taiwan Normal University
Hsin-Han Lee
Hsin-Han
Lee
Academia Sinica
Naohisa Wada
Naohisa
Wada
Kyushu University
Academia Sinica
Kyushu University Hospital
Wei-An Liu
Wei-An
Liu
Academia Sinica
Min R. Lu
Min R.
Lu
Academia Sinica
Cheng-Kuo Lai
Cheng-Kuo
Lai
National Taiwan University
Academia Sinica
Huei-Mien Ke
Huei-Mien
Ke
Academia Sinica
Pei-Feng Sun
Pei-Feng
Sun
Academia Sinica
National Taiwan Normal University
Sen-Lin Tang
Sen-Lin
Tang
Academia Sinica
National Taiwan Normal University
Wen-Hsin Chung
Wen-Hsin
Chung
National Chung Hsing University
Ying-Lien Chen
Ying-Lien
Chen
National Taiwan University
Chia-Lin Chung
Chia-Lin
Chung
National Taiwan University
Isheng Jason Tsai
Isheng Jason
Tsai
0000-0002-2123-5058
National Taiwan University
Academia Sinica
National Taiwan Normal University
Comparative genomic and transcriptomic analyses of trans-kingdom pathogen Fusarium solani species complex reveal degrees of compartmentalization
Abstract Background The Fusarium solani species complex (FSSC) comprises fungal pathogens responsible for mortality in a diverse range of animals and plants, but their genome diversity and transcriptome responses in animal pathogenicity remain to be elucidated. We sequenced, assembled and annotated six chromosome-level FSSC clade 3 genomes of aquatic animal and plant host origins. We established a pathosystem and investigated the expression data of F. falciforme and F. keratoplasticum in Chinese softshell turtle (Pelodiscus sinensis) host. Results Comparative analyses between the FSSC genomes revealed a spectrum of conservation patterns in chromosomes categorised into three compartments: core, fast-core (FC), and lineage-specific (LS). LS chromosomes contribute to variations in genomes size, with up to 42.2% of variations between F. vanettenii strains. Each chromosome compartment varied in structural architectures, with FC and LS chromosomes contain higher proportions of repetitive elements with genes enriched in functions related to pathogenicity and niche expansion. We identified differences in both selection in the coding sequences and DNA methylation levels between genome features and chromosome compartments which suggest a multi-speed evolution that can be traced back to the last common ancestor of Fusarium. We further demonstrated that F. falciforme and F. keratoplasticum are opportunistic pathogens by inoculating P. sinensis eggs and identified differentially expressed genes also associated with plant pathogenicity. These included the most upregulated genes encoding the CFEM (Common in Fungal Extracellular Membrane) domain. Conclusions The high-quality genome assemblies provided new insights into the evolution of FSSC chromosomes, which also serve as a resource for studies of fungal genome evolution and pathogenesis. This study also establishes an animal model for fungal pathogens of trans-kingdom hosts.
Microbiology
Genetics
figshare
2022
2022-10-21
2022-10-21
Collection
10.1186/s12915-022-01436-7
CC BY 4.0